WGS based analysis of acquired antimicrobial resistance in human and non-human Acinetobacter baumannii isolates from a German perspective

BACKGROUND: Acinetobacter baumannii ability to develop and acquire resistance makes it one of the most critical nosocomial pathogens globally. Whole-genome sequencing (WGS) was applied to identify the acquired or mutational variants of antimicrobial resistance (AMR) genes in 85 German A. baumannii strains utilizing Illumina technology. Additionally, the whole genome of 104 German isolates deposited in the NCBI database was investigated. RESULTS: In-silico analysis of WGS data revealed wide varieties of acquired AMR genes mediating resistance mostly to aminoglycosides, cephalosporins, carbapenems, sulfonamides, tetracyclines and macrolides. In the 189 analyzed genomes, the ant (3″)-IIa conferring resistance to aminoglycosides was the most frequent (55%), followed by bla(ADC.25) (38.6%) conferring resistance to cephalosporin, bla(OXA-23) (29%) and the bla(OXA-66) variant of the intrinsic bla(OXA-51-likes) (26.5%) conferring resistance to carbapenems, the sul2 (26%) conferring resistance to sulfonamides, the tet. B (19.5%) conferring resistance to tetracycline, and mph. E and msr. E (19%) conferring resistance to macrolides. bla(TEM) variants conferring resistance to cephalosporins were found in 12% of genomes. Thirteen variants of the intrinsic bla(OXA-51) carbapenemase gene, bla(OXA-510) and bla(ADC-25) genes were found in isolates obtained from dried milk samples. CONCLUSION: The presence of strains harboring acquired AMR genes in dried milk raises safety concerns and highlights the need for changes in producing dried milk. Acquired resistance genes and chromosomal gene mutation are successful routes for disseminating AMR determinants among A. baumannii. Identification of chromosomal and plasmid-encoded AMR in the genome of A. baumannii may help understand the mechanism behind the genetic mobilization and spread of AMR genes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-021-02270-7.